Move php-mode and mmm-mode into site-lisp/

If I can move all third-party libs in there, things will be a bit easier
to wrangle.
Move web-mode into site-lisp
Update web-mode from current master
Move git-commit-mode subtree into site-lisp
Move flymake-related libraries into site-lisp/
Move jedi-related packages into site-lisp
Move yasnippet to site-lisp/
Move js-mode-related libraries into site-lisp/
Merge branch 'add-site-lisp-dir' into emacs-24

One small step towards a slightly-more organized .emacs.d/.